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Sustainable Fisheries

Background rationale

Steadily depleting wild fish stocks and growing consumer demand for fish products mean that the aquaculture of marine species could become an increasingly important food source and economic activity within the European Union. The potential expansion of the aquaculture sector is recognized and supported by the European Parliament (Guillot, 2010), however any such development must be sustainable and regulated with respect to biosafety, including possible risks to the environment (European Commission, 2009). One aspect of environmental risk associated with marine fish aquaculture is the potential impact of releasing farmed fish into the wild, through accidental escape (Bekevold et al., 2006; Svasand et al., 2007) or deliberate restocking (Bell et al., 2008). Such releases raise issues relating to the spread of disease, ecological disruption and changes to the genetic make-up of wild stocks. In contrast to the large investment in management of farmed fish, including research and technology development (RTD), little information is available on the fate of escapees, in terms of their fitness, breeding success or distribution. Knowledge about the fate of farm escapees is however crucial as interbreeding with individuals from wild populations leads to genetic introgression, the introduction of gene alleles from farmed animals into wild populations, a process implying considerable risks.

The major risks, loss of genetic diversity within populations; loss of genetic diversity among populations; loss of fitness, although known for several decades, are difficult to predict. A rule of thumb is that if farmed escapees comprise more than 10% of successful spawners, overall effective population size will not be much larger than the effective size of the captive broodstock. Moreover, while in the past typically low levels of genetic divergence in many marine fish were assumed, several recent studies show strong evidence for local adaptations of marine species,  including mobile and highly fecund fishes like Atlantic cod (Harald et al., 2010). Escape of farmed fish thus poses a significant threat to locally adapted populations, even on local scales.

To manage and mitigate risks, and to assess the impact of releases, it is important to be able to characterize, distinguish and identify farmed and wild individuals. The ability to trace-back fish to a farmed origin also has applications to product label authentication. Escapes of fish from sea-cages have been reported for almost all species presently cultured across Europe, including Atlantic salmon, Atlantic cod, rainbow trout, Arctic charr, halibut, sea bream, sea bass and meagre. In comparison to Atlantic salmon, knowledge of the extent and effect of escapes of Atlantic cod is very limited. Also for other culture species, like sea bream, sea bass and meagre, knowledge regarding identification of escaped fish and how escapes might affect to local fisheries is virtually non-existent (Moe et al., 2007). The use of DNA technology to identify the origin of fish is now widely implemented (Ogden, 2008) but its application to the issue of farmed origin has to date been mainly limited to salmonids (Glover et al., 2008). With an increasing range of marine fish now subject to aquaculture operations, there is a need to evaluate methods for the genetic assignment of fish to either a farmed or wild source and, where possible, to determine the precise genetic population of origin.


Identification issues

In contrast to salmonids there are various challenges to identifying marine fish as originating from aquaculture or wild populations and even more when considering their hatchery of origin:

  • Due to the recent domestication of many marine fish, allele frequencies of broodstock and their offspring remain similar to natural populations.
  • The lack of targeted selective breeding for cod and especially sole, lowers the likelihood to find "domestication" markers, unambiguously identifying fishes originating from a farm or hatchery. Many fish farms are only at the first generation of breeding, coinciding with the genetic background of offspring similar to that of natural populations. However, several new developments and peculiarities of marine fish aquaculture, aid in the identification of a farmed individual.
  • Due to the use of mass spawning in breeding tanks and the very high variance in reproductive success of parents in hatcheries (Porta et aI., 2006 a,b, 2007), genetic diversity of offspring is usually much lower than parental populations and natural population offspring in the wild. As such first generation escapees or restocking material will exhibit a very low individ ual heterozygosity level (MLH) compared to outbred natural populations.
  • Additionally, based on recent results of natural population genotyped for 450+ (sole) and 1300+ (cod) SNPs, farmed offspring would be easily identified if exported outside their region of origin, using genetic assignment tools.
  • For both species, a large panel of individuals from natural populations, potential sources for aquaculture purposes, is available genotyped for a large number of SNPs and microsatellites. As such simulation studies can be applied to assess the power of both marker types in assigning aquaculture vs natural origin, besides tracing individuals to the hatchery of origin.
  • Finally, the rate of fixation of neutral markers depends on the effective population size of breeding populations, but SNPs under positive/negative selection can increase the rate of fixation and thus form ideal candidate domestication markers. Additionally, such markers may introgress more rapidly/slowly than selectively neutral markers, providing crucial insights into the fitness and molecular consequences of restocking/escapees in natural populations.

These issues combine to form several lines of research to be addressed within AquaGen. Collectively, this work presents an excellent opportunity to develop a research framework and set of management tools required for an expansion of marine fish aquaculture in the EU.

The stated aims of AquaGen are to:

  1. Evaluate the feasibility of distinguishing genetically between farmed and wild common sole and Atlantic cod;
  2. Evaluate the feasibility of genetically tracing individual fish back to a farmed origin, - ideally to the farm of origin -, in common sole and Atlantic cod;
  3. Develop appropriate identification methodologies, including a comparison of population assignment methods with parentage identification techniques, to provide the greatest power for correctly identifying farmed individuals;
  4. Develop traceability assays within a forensic framework (standard operating procedures) in order to ensure that the assays can be applied in a legal context;
  5. Examine the applicability of the approach to other marine aquaculture species, particularly farmed in the Mediterranean, e.g. European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata).

AquaGen will achieve these aims by utilizing the genetic resources developed during the EU's FP7 project FishPopTrace (EC: 212399), combined with samples of farmed fish from the two target species. Methods of assignment will be evaluated using real and simulated genetic data to optimise the design of robust traceability assays. The work will be placed in a broader context of marine fish aquaculture management through the delivery of a critical literature review to ensure that conclusions regarding genetic traceability tools are applicable across species.